update package tests

Author: mansouralawi

exm/align/align.py

@@ -12,7 +12,7 @@
 from typing import Tuple, Optional, List
 
 from exm.args import Args
-from exm.io.io import nd2ToVol , get_raw_volume
+from exm.io.io import nd2ToVol
 from exm.utils import chmod, subtract_background_rolling_ball, subtract_background_top_hat,downsample_volume, enhance_and_filter_volume
 
 from exm.utils import configure_logger

tests/conftest.py

@@ -4,39 +4,40 @@
 import numpy as np
 
 def setup_dataset():
-    # Define the directories
-    base_dir = os.path.join(os.environ.get("BASE_DIR"),'dataset')
+    # Define the base directory
+    base_dir = os.path.join(os.environ.get("BASE_DIR"), 'dataset')
 
+    # Define the code directories
     dir_names = ["code0", "code1", "code2"]
 
     # Create directories
     for dir_name in dir_names:
         os.makedirs(os.path.join(base_dir, dir_name), exist_ok=True)
 
-
     # Function to create the volume with a white center and optional shift
     def create_volume(shift_x=0, shift_y=0, shift_z=0):
         volume = np.zeros((10, 10, 10), dtype=np.uint16)
-        volume[4+shift_x:7+shift_x, 4+shift_y:7+shift_y, 4+shift_z:7+shift_z] = 65535
+        volume[4 + shift_x:7 + shift_x, 4 + shift_y:7 + shift_y, 4 + shift_z:7 + shift_z] = 65535
         return volume
 
     # Create .h5 files with the modified properties
     shifts = [(0, 0, 0), (1, 0, 0), (0, 1, 0)]  # No shift, shift in x, shift in y
-    channels = ['640','594','561','488','405']
+    channels = ['640', '594', '561', '488', '405']
+
     for dir_index, dir_name in enumerate(dir_names):
-        for i,channel in zip(list(range(5)),channels):
-            file_path = os.path.join(base_dir, f"code{dir_index}/Channel{channel} SD_Seq000{i}.h5")
-            
-            # Create the volume with the appropriate shift
-            volume = create_volume(*shifts[dir_index])
-            
-            # Save the volume in the .h5 file
+        for fov_index in range(1):  # Create 5 FOV files per code directory
+            file_path = os.path.join(base_dir, f"{dir_name}/raw_fov{fov_index}.h5")
+
+            # Create an empty volume and populate it with channels
             with h5py.File(file_path, 'w') as f:
-                dataset_name = f"{channel}"
-                f.create_dataset(dataset_name, data=volume)
+                for channel in channels:
+                    # Create the volume with the appropriate shift
+                    volume = create_volume(*shifts[dir_index])
+                    dataset_name = f"{channel}"
+                    f.create_dataset(dataset_name, data=volume)
 
 def cleanup_dataset():
-    base_dir = os.path.join(os.environ.get("BASE_DIR"),'dataset')
+    base_dir = os.path.join(os.environ.get("BASE_DIR"), 'dataset')
     shutil.rmtree(base_dir, ignore_errors=True)
 
 def pytest_sessionstart(session):